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Even with significant developments in nanoscience, relatively little is known about the interactions of nanocrystal semiconducting materials with bio-macromolecules. To investigate the interfacial phenomena of cadmium selenide quantum dot (CdSe QD) nanocrystals with proteins extracted from Moringa oleifera seeds, different concentrations of cadmium selenide quantum dots–Moringa oleifera seed protein (CdSe–MSP) complexes were prepared. Respective CdSe QDs with hexagonal phase and crystalline size in the range of 4–7 nm were synthesized and labelled with the purified mesoporous MSP having a surface area of 8.4 m2/g. The interaction mechanism between CdSe QDs and MSP was studied using UV–Vis absorption, fluorescence emission and Fourier Transform Infrared spectroscopies. The UV–Vis absorption spectra showed absorption bands of CdSe–MSP complexes at 546.5 nm. The fluorescence intensity of CdSe QDs was found to decrease with increasing concentration of MSP. The thermodynamic potentials ∆Hθ (−321.3 × 103 Jmol−1); ∆Sθ (156.0 JK−1mol−1) and ∆Gθ (−46.6 × 103 Jmol−1) were also calculated. The stability of the complex found is strongly influenced by electrostatics interaction and surface-bound complexation equilibrium attraction. This information can help to elucidate the surface characteristics of MSP and its potential interactions with other molecules or nanoparticles.